Mechanistic insights into human pre-mRNA splicing of human ultra-short introns

Potential unusual mechanism identifies G-rich introns

Noriko Sasaki-Haraguchi, Makoto K. Shimada, Ichiro Taniguchi, Mutsuhito Ohno, Akila Mayeda

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

It is unknown how very short introns (<65 nt; termed 'ultra-short' introns) could be spliced in a massive spliceosome (>2.7. MDa) without steric hindrance. By screening an annotated human transcriptome database (H-InvDB), we identified three model ultra-short introns: the 56-nt intron in the HNRNPH1 (hnRNP H1) gene, the 49-nt intron in the NDOR1 (NADPH dependent diflavin oxidoreductase 1) gene, and the 43-nt intron in the ESRP2 (epithelial splicing regulatory protein 2) gene. We verified that these endogenous ultra-short introns are spliced, and also recapitulated this in cultured cells transfected with the corresponding mini-genes. The splicing of these ultra-short introns was repressed by a splicing inhibitor, spliceostatin A, suggesting that SF3b (a U2 snRNP component) is involved in their splicing processes. The 56-nt intron containing a pyrimidine-rich tract was spliced out in a lariat form, and this splicing was inhibited by the disruption of U1, U2, or U4 snRNA. In contrast, the 49- and 43-nt introns were purine-rich overall without any pyrimidine-rich tract, and these lariat RNAs were not detectable. Remarkably, shared G-rich intronic sequences in the 49- and 43-nt introns were required for their splicing, suggesting that these ultra-short introns may recruit a novel auxiliary splicing mechanism linked to G-rich intronic splicing enhancers.

Original languageEnglish
Pages (from-to)289-294
Number of pages6
JournalBiochemical and Biophysical Research Communications
Volume423
Issue number2
DOIs
Publication statusPublished - 29-06-2012

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RNA Precursors
Introns
Genes
U2 Small Nuclear Ribonucleoproteins
Protein Splicing
NADP
Transcriptome
Cultured Cells
Screening
Oxidoreductases
Cells
Databases
RNA

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

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abstract = "It is unknown how very short introns (<65 nt; termed 'ultra-short' introns) could be spliced in a massive spliceosome (>2.7. MDa) without steric hindrance. By screening an annotated human transcriptome database (H-InvDB), we identified three model ultra-short introns: the 56-nt intron in the HNRNPH1 (hnRNP H1) gene, the 49-nt intron in the NDOR1 (NADPH dependent diflavin oxidoreductase 1) gene, and the 43-nt intron in the ESRP2 (epithelial splicing regulatory protein 2) gene. We verified that these endogenous ultra-short introns are spliced, and also recapitulated this in cultured cells transfected with the corresponding mini-genes. The splicing of these ultra-short introns was repressed by a splicing inhibitor, spliceostatin A, suggesting that SF3b (a U2 snRNP component) is involved in their splicing processes. The 56-nt intron containing a pyrimidine-rich tract was spliced out in a lariat form, and this splicing was inhibited by the disruption of U1, U2, or U4 snRNA. In contrast, the 49- and 43-nt introns were purine-rich overall without any pyrimidine-rich tract, and these lariat RNAs were not detectable. Remarkably, shared G-rich intronic sequences in the 49- and 43-nt introns were required for their splicing, suggesting that these ultra-short introns may recruit a novel auxiliary splicing mechanism linked to G-rich intronic splicing enhancers.",
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Mechanistic insights into human pre-mRNA splicing of human ultra-short introns : Potential unusual mechanism identifies G-rich introns. / Sasaki-Haraguchi, Noriko; Shimada, Makoto K.; Taniguchi, Ichiro; Ohno, Mutsuhito; Mayeda, Akila.

In: Biochemical and Biophysical Research Communications, Vol. 423, No. 2, 29.06.2012, p. 289-294.

Research output: Contribution to journalArticle

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AU - Sasaki-Haraguchi, Noriko

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